Adam wakes up in the other stasis pod and hauls himself out. Pritchard re-establishes contact with him and says that he was out for several days, and that his transponder shows that he's in Singapore.
He tells Adam that something is jamming the latter's GPL signal, and to find the source and disable it. Adam makes his way through a nearby building and disables the jammer. Pritchard calls back to reveal that his and three other Sarif scientist's signals have appeared. Adam tells him to relay the information to Sarif, but Pritchard says that while he was asleep, Taggart, Sarif and many United Nations delegates all left with Darrow to go to Panchaea for the official site launch.
Adam tracks the signals and eventually encounters Dr. Declan Faherty in one of the laboratories. Faherty expresses surprise at Adam's condition, and they discuss Sevchenko's death and the scientists' work. Faherty tells him that he was working on a biochip that could broadcast software upgrades directly into a person's neural circuitry. He also tells Adam that Megan is in a secured zone, and the agent suggests setting off an explosion in one of the labs to draw the troops away so he can get in.
They eventually agree to set off a series of explosions to cover the escape. Faherty says that in order to fool Belltower, he should also talk to one of the other captured scientists to jam the GPL signals.
Adam continues through the labs and eventually comes across Dr. Nia Colvin, who initially tries to defend Belltower's practices before Adam convinces her to follow his plan. Soon after, he finds Dr. Koss and convinces him to set off his own explosion. Koss gives him a copy of a virus to upload which will disable the GPL implants.
After reaching the central security mainframe, Adam uploads the virus and alerts Pritchard to send a signal that will make the GPL implants vibrate. Soon after, the scientists set off the three explosions and the Belltower troops are drawn away from the secured zone. Adam takes a nearby elevator down and accesses the restricted area.
He emerges into a exhibit of animated human anatomy models. Zhao appears and confronts him over his actions. Adam says that he's figured out the conspiracy and brings up the biochip, which he realizes acts like a killswitch. He reasons that Zhao is afraid of augmented people like him.
Zhao pulls out a control device and attempts to activate the upgraded biochip in Adam's head... except that nothing happens because it was never installed. Adam mocks her for believing he received the upgrade while she freaks out and runs away. Suddenly, Namir reveals himself to be one of the anatomy models and attacks Adam.
A fight ensues between the two augs. Adam eventually smashes Namir through a pane of glass and into a wall, mortally wounding him. Namir tells him to finish it, and tells the agent that men like them never get back the things they love before he passes away.
Adam continues into a white room and discovers Megan, who is working at her desk. After she expresses shock at seeing him, he angrily asks her if she's part of the conspiracy. She says that the kidnapping and attack was real. She tells him that she wanted to reveal the truth about her research before - it was based off of his DNA samples. She says that Sarif convinced her to reveal the research, but Hugh Darrow convinced her otherwise by bringing her to the Singapore facility.
He realizes what it means and tells Pritchard to contact Sarif and let him know about Darrow's duplicity. Megan attempts to stop him and says that Darrow was tricking Tai Yong and the other conspirators, and that the biochip control signal doesn't work. He tells her that the signal did work, and it's what Zhao is attempting to use to control the population.
At that moment, a broadcast begins on Panchaea. Darrow thanks the delegates for coming out and says that he wants to show the world how augmentation can change the world. He tells the audience to forgive him and activates the signal, which causes everyone in the world with an upgraded biochip to turn crazed and attack each other. Adam tells Megan that he's going back to find the scientists in the complex, but she tells him that she will find them and bring them to the nearby helipad.
Malik radios him as he heads to the helipad and reveals that she's on her way. When he arrives, he sees that several of the scientists in the area have been affected by the signal before activating the helipad's roof. Malik arrives and knocks out the crazed scientists with an EMP grenade before Megan and the others escape on her VTOL.
Megan radios and tells him to stop Darrow's broadcast. She informs him that there's a shuttle in the helipad that can reach Panchaea and orders him to get inside. He accesses the shuttle and it launches from the base.
The shuttle travels on a sub-orbital trajectory and nears Panchaea. Suddenly, the shuttle experiences a system failure and crashes into the water near the platform...
- Book-Ends: The mission is the inverse of the prologue - instead of the mercenaries attacking Sarif to capture the scientists, this time it's Adam assaulting Omega Ranch to rescue them.
- The Cavalry: Malik shows up to take out all the scientists at the helipad, provided that she was rescued during the "Return to Hengsha" mission.
- Coming in Hot: The systems onboard the rocket fail just as it enters the atmosphere aboard Panchaea and crashes. Notably, this is the only major equipment failure (not caused by enemies) that occurs in the game.
- Defrosting Ice King: Pritchard becomes a lot more likable and receptive to Adam's demands after he discovers the full extent of what happened to the scientists, and genuinely seems concerned for his welfare.
- Expospeak Gag: One email in the Ranch goes into a technical explanation for people applying pressure to office equipment, before cutting straight to the point and telling them to stop breaking things by sitting on them with "their fat asses".
- 419 Scam: Played for Laughs. One of the computers in the ranch has a message from a worker asking why they keep receiving scam emails even though they're supposed to be in a top-secret operation.
- Full-Frontal Assault: Namir is completely naked for his fight with Jensen, as a result of using his heavily augmented body's unique appearance to hide among the anatomy statues in the room.
- Gameplay and Story Segregation: It's possible to knock out Namir with a single punch or otherwise incapacitate him non-lethally, but when the post-fight cutscene occurs, he seemingly dies from internal injuries after a conversation with Adam. This was likely a bug, as it was fixed for the Director's Cut release.
- Hidden in Plain Sight: Namir is posing among the anatomy models when Adam confronts Zhao.
- Interface Screw: If the Tai Tong biochip upgrade was taken beforehand, Adam suffers from this for the duration of the Namir fight before Megan repairs his systems.
- Ironic Echo:
- "Women never fail to underestimate men."
- Adam throws Namir through a pane of glass to defeat him, much like Namir did to him in the prologue mission.
- Oh, Crap!: Zhao, if the player hasn't chosen the new biochip.
- Painting the Medium: When Jensen wakes up in the pod, the edges of the 'camera' are notably coated with frost.
- P.O.V. Cam: In the (otherwise third-person) cutscene before the fight with Namir, if Jensen's biochip was upgraded, Jensen's vision briefly switches to first-person to show his HUD glitching out after Zhao activates the biochip. Happens again afterwards in the conversation between Adam and Megan, when she injects him with a neuro-suppressor that disables the control signal.
- Soft Glass: When Namir is kicked through the display, it easily shatters from the force of impact, despite being much more resilient during the boss battle that preceded it.
- Stockholm Syndrome: Nia (and possibly Megan) both show shades of this, with the former initially defending Belltower's experiments in spite of the fact that her co-worker was murdered by them, and the latter responding a bit too... friendly towards Namir when Adam enters the room.
- Wham Episode: Darrow betrays everyone, causing the augmented with new biochips to go on a psychotic rampage.
- What the Hell, Hero?: Nia initially calls out Adam for failing to protect the scientists during the Sarif attack. However, she apologizes for it after once she realizes the extent of Belltower's brutality.
- Woman in White: Megan is seen working in an all-white room.